The UK government’s new border regime to tackle Covid-19 came under increasing strain on Friday, with its quarantine hotel booking system down for a second day and growing concerns over how the scheme will work.

Anyone arriving in England from 33 high-risk countries will from Monday have to book into a government-approved hotel to self-isolate under supervision for 10 days, in response to fears that dangerous variants of Covid-19 could be imported from abroad.

But the government booking website went down shortly after its launch on Thursday afternoon and was offline for more than 24 hours until late on Friday afternoon.

The government contracted Australia-headquartered Corporate Travel Management to help it set up the managed quarantine system, including the troubled website. The company declined to comment.

A picture of frantic final preparations emerged on Friday, as airlines, airports and hotels waited to hear how parts of the policy would be implemented.

Border Force agents will be expected to identify travellers who need to be moved to hotels, but by Friday afternoon the agency had not been given any guidance on how the system would work, according to Yvette Cooper, chair of the House of Commons home affairs select committee.

“We can’t afford chaotic arrangements like this as it makes it easier for new variants to spread,” Cooper said.

Border Force did not immediately respond to a request for comment.

At least one airport had not been told which hotels passengers needed to be sent to, while hotels that had offered their services for the quarantine scheme complained of “unanswered questions” and said plans were “still not massively clear".

How much time travellers would be allowed outside, whether they could smoke and when and how staff would be tested were questions still under discussion on Friday.

A government document explaining the policy to hotels seen by the Financial Times had a note saying “this is changing” under guidelines outlining when people could leave their room, such as for exercise.

When questioned why the government had chosen not to implement as strict measures as Australia, Downing Street said: “The rules are in line with other countries who are taking this approach.”

Amid growing concerns among trade unions over the safety of hotel and security staff, the government guidelines said hotels must manage any positive outbreaks of coronavirus among staff.

Bryan Simpson, hospitality organiser for Unite the Union, said: “The revelations that the UK’s guidelines for preventing the transmission of Covid are far inferior to those in Australia are deeply alarming for hotel workers.”

A government spokesperson said: “Strict hygiene and infection control measures will be in place, all staff will be fully trained in Covid secure practices.”

There is some sympathy in Whitehall for Matt Hancock, health secretary, who was left to organise the hotel quarantine system after other government departments insisted it was not their responsibility. “It was a hot potato nobody wanted,” said one senior official.

Aviation executives said the government faced a difficult logistical exercise, but warned that they expected disruption on Monday.

The current policy only applies to England, although the Welsh and Northern Irish devolved administrations are expected to implement similar rules. The Scottish government has indicated it will go further and require all people arriving from any country outside the UK’s common travel area with Ireland to go into the hotels.

The problems are the latest blow to a policy that has been criticised by some parts of the Conservative party and from within the travel industry.

It has also emerged there was a heated discussion between test providers and the government on Thursday over the new plan to test people returning to the UK on days two and eight after arrival, according to several people who were present.

More than 100 people from testing companies, laboratories and private doctors’ clinics were on a call with officials to iron out the details of the plan, that was described as “fractious” and a “debacle”.

Under the plan put forward by the department of health, the NHS will offer a £210 package of two tests on day two and day eight after arrival from next week. Private providers are expected to enter the market at the start of March.

The day two test will be sent off for genomic sequencing if it comes back positive, so the government can determine which variant of the virus individuals have been infected with.

But several private companies and labs said it would be near impossible for them to step in from March and compete with the £210 NHS package, particularly as almost all of them do not have genomic sequencing capabilities, according to one executive who was present.